[gmx-users] Disappear my solution

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 28 16:11:01 CEST 2008

Morteza Khabiri wrote:
> Dear
> Thanks for your prompt reply.
> In gro file everything is ok. during the run I just load my XTC file by
> vmd visual software and i saw that after 1.3 ns suddenly hexan disappear

Did you restart your run after that short time?  Did you change the xtc-grps 
option in your .mdp file?

> and my system just have protein and water. the most strange things is that
> the place of hexan is empty and is not full by water. I think that the
> molecule are in their place but maby vmd could not visualize them. On the

That would be pretty strange.  If they were there, then disappeared, maybe they 
were not written to the .xtc.

> other hand the program is running but the number of frame is not change.

If the frame number is not changing, it is done loading the trajectory, or it 
has encountered a problem.  Are there any error messages in the VMD console? 
I'm thinking that you've not written the hexane coordinates to the .xtc file, 
and now VMD is failing because the number of coordinates in the trajectory no 
longer corresponds to the number of atoms in the structure file.


> Thanks for your help
> Yours,
> Morteza
> Ph.D student of Biophysics
> Laboratory of High performance computing
> Institute of Systems Biology and Ecology ASCR
> Institute of Physical Biology,
> University of South Bohemia
> Zamek 136 373 33, Nove Hrady
> Czech Republic
> Email: Khabiri at greentech.cz
> mobile: +420 773 903 109
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list